well, it depends...

for commuting, the main disadvantage is that you have to change shoes - or else do whatever it is in cycling shoes which for most people at work doesn't cut it... but much of the time you change shoes anyway if there is a threat of rain of mud and/or you have to wear nice shoes at work. If you already change shoes, then clipless for commuting will bring benefits w/ few drawbacks. learning clipless is generally not that hard -- usually the first day is difficult and then you get used to it and then some time in the first few weeks after you stop "concentrating" then you forget and fall once or twice while stopped or talking to someone or whatever... for the basic SPDs you can adjust then so they are really loose when you start.

i have 4 bikes total and for my main commuter that i use to ride to work (10km each way) i have clipless pedals. i also have an old bike with clips/cages that i sometimes use for really short trips for shopping or when i don't want to change shoes. a few years ago i had a 1 mile commute and then i rode w/o clipless b/c it would take longer to change shoes than to ride a mile, so it wasn't worht it. plus i have an extra set of flat pedals that i can change out on my main commuter but i only do maybe once a year for something special.